The determination of the mouse genome sequence will provide crucial data to understand the human genome. The first step in that process will be a determination of a rough draft of the human genome. We have developed a small, highly flexible genome center with an extremely strong informatics component. This infrastructure will allow us to rapidly and efficiently take advantage of the new capillary sequencers available, without a major loss due to a large gel-based sequencing operation that must be utilized. As a result, we will be able to scale our operation from roughly 6000 reads per week currently to 48,000 reads per week in a year and then double once again to about 100,000 reads per week by the end of the third year. This ramp rate will allow us to produce about 700 megabases of rough draft sequence over 3 years. While this is being accomplished, we will be developing software to accelerate the finishing process. This software will allow some of the same process flow tools we use in production to be applied to finishing. This, when coupled to software for automated editing developed at other sites should lead to a 5-10 fold increase in per capita finishing rates. This will allow us to finish the mouse rough draft sequence we produce now in the second phase of the project, in a cost effective, timely fashion.